GSE110096

Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

6 case / 3 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Source: GEO
Assay: bulk RNA-seq
Organism: Mus musculus
Whole-study samples: 9 samples
Specimen: Tissue
Reported/interpreted study design: Treatment vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Zhang H, Chen Q, Zhang G
Contact name: Qingshan Chen
Submission date: 2018-02-02
Last update: 2021-02-02
Organization: Third Affiliated Hospital of Second Military Medical University
Department: Not available
Public date: 2021-02-02
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL18635 Ion Torrent Proton (Mus musculus)
Series type: Series
SubSeries: Not available
BioProject: PRJNA432742

Summary

Transcriptome analysis is an effective method to study a comprehensive understanding of molecular mechanisms involved in biological processes and diseases by RNA-Sequencing (RNA-Seq). This study aimed to elucidate the possible mechanisms of Schisandrin B on CCl4-induced liver fibrosis through detecteing hepatic gene expression profiles by RNA-Seq.

Overall design

Liver mRNA profiles of normal, liver fibrosis, Schisandrin B treated rtas were generated by deep sequencing, in triplicate.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 9 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	No match found
Expression Atlas	Planned source for curated expression experiment links.	No match found
PubMed	Primary GEO citations and related PubMed articles that mention this dataset. 1 linked publication 1 DOI Related publications Mechanical stiffness orchestrates distinct regulation of MRTFs and YAP/TAZ transcriptional cofactors in hepatocytes. The FEBS journal, 2026 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

100 pts

Clarity: 100%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Review before analysis

78% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

3/15 pts

Unassigned or review-needed samples remain before analysis.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

3 samples need manual grouping review.
Critical dataset warnings must be resolved.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.
Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Needs review

3 review-needed samples and 0 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

One or more samples were flagged for manual review.

Critical dataset warnings are present.

Why This Is Ranked Here

Tumor vs normal

Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Organism differs from search intent Mus musculus Search intent expects Homo sapiens. Organism came from Normalization rules.
Disease context Fibrosis, liver fibrosis Disease context came from Normalization rules.
Likely case group Treated 6 samples
Likely control group Normal tissue 3 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded for tissue search because it is a treatment/control experiment. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Fibrosis, Liver fibrosis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 42080703.
Publication context: Mechanical stiffness orchestrates distinct regulation of MRTFs and YAP/TAZ transcriptional cofactors in hepatocytes.. The FEBS journal, 2026. PMID 42080703. DOI 10.1111/febs.70570.

Cautions

Downgraded for tissue search because it is a treatment/control experiment.
Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because non-human datasets are outside the selected human ranking intent.
Overall score capped because fewer than ten samples limit cohort confidence.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Treated samples may need review depending on the comparison.
Dataset organism does not match the human patient-tissue tumor-normal intent.

Normalized Fields

35 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source liver GSM2977565 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM2977566 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM2977567 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM2977568 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM2977569 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM2977570 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM2977571 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM2977572 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM2977573 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE110096 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE110096 dataset_title: Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing organism: Mus musculus ass... keyword match keyword match: bulk rna-seq

disease fibrosis GSE110096 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis dataset_accession: GSE110096 dataset_title: Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing organism: Mus musculus ass... controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSE110096 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis dataset_accession: GSE110096 dataset_title: Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing organism: Mus musculus ass... controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM2977568 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis N23 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM2977568 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis N23 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM2977569 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis N24 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM2977569 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis N24 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM2977570 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis N32 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM2977570 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis N32 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary disease match: liver fibrosis

organism Mus musculus GSE110096 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence mus musculus dataset_accession: GSE110096 dataset_title: Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing organism: Mus musculus ass... keyword match keyword match: mus musculus

sample_type normal tissue GSM2977571 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal N36 normal liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: none controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM2977572 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal N37 normal liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: none controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM2977573 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal N39 normal liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: none controlled vocabulary controlled vocabulary sample type match: normal

tissue liver GSE110096 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver dataset_accession: GSE110096 dataset_title: Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing organism: Mus musculus ass... controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977565 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N18 Schisandrin B treated liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: Schisandrin B treated liver controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977566 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N20 Schisandrin B treated liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: Schisandrin B treated liver controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977567 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N22 Schisandrin B treated liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: Schisandrin B treated liver controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977568 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N23 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977569 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N24 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977570 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N32 Liver fibrosis liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: liver fibrosis controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977571 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N36 normal liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: none controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977572 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N37 normal liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: none controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM2977573 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver N39 normal liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: none controlled vocabulary controlled vocabulary tissue match: liver

treatment_status treated GSM2977565 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence treated N18 Schisandrin B treated liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: Schisandrin B treated liver controlled vocabulary controlled vocabulary treatment status match: treated

treatment_status treated GSM2977566 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence treated N20 Schisandrin B treated liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: Schisandrin B treated liver controlled vocabulary controlled vocabulary treatment status match: treated

treatment_status treated GSM2977567 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence treated N22 Schisandrin B treated liver tissue: liver; strain: Wistar rat; treatment time: 8 weeks; treatment: Schisandrin B treated liver controlled vocabulary controlled vocabulary treatment status match: treated

Sample Group Preview

9 rows shown Show Hide

Study totals: Case 6 | Control 3 | Unassigned 0 | Excluded 0 | Ambiguous 0 9 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Treated	Case	GSM2977565	N18	Schisandrin B treated liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: Schisandrin B treated liver	treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated	Case	GSM2977566	N20	Schisandrin B treated liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: Schisandrin B treated liver	treated sample: Treated sample may need exclusion outside treatment comparisons.
Treated	Case	GSM2977567	N22	Schisandrin B treated liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: Schisandrin B treated liver	treated sample: Treated sample may need exclusion outside treatment comparisons.
Liver fibrosis	Case	GSM2977568	N23	Liver fibrosis liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: Liver fibrosis	Case marker detected.
Liver fibrosis	Case	GSM2977569	N24	Liver fibrosis liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: Liver fibrosis	Case marker detected.
Liver fibrosis	Case	GSM2977570	N32	Liver fibrosis liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: Liver fibrosis	Case marker detected.
Normal tissue	Control	GSM2977571	N36	Normal liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: None	Control marker detected.
Normal tissue	Control	GSM2977572	N37	Normal liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: None	Control marker detected.
Normal tissue	Control	GSM2977573	N39	Normal liver Tissue: Liver; Strain: Wistar rat; Treatment time: 8 weeks; Treatment: None	Control marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.

Summary

Overall design

Source Evidence

Related publications

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort